Difference between revisions of "Team:Valencia UPV/Model"

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<h4 style="color:#005368; padding-left: 20px !important;">INDEX</h4>
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<ul class="list-group list-unstyled">
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<li class="list-group-item active">
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<a class="dropdown-toggle" href="#intro">Introdiction</a>
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<ul>
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<li><a href="#deterystcomod">Deterministic and Stochastic Models</a></li>
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</li>
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<li class="list-group-item">
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<a class="dropdown-toggle" href="#overview">Overview</a>
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<ul>
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<li><a href="#what">What We Are Modeling?</a></li>
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<li><a href="#software">Modeling Software Modules</a></li>
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</ul>
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</li>
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<li class="list-group-item">
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<a class="dropdown-toggle" href="#HPoptcir">Human-Plant: Optogenetic Circuit</a>
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<ul>
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<li><a href="#HPdeter">Deterministic</a></li>
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<li><a href="#HPstoch">Stochastic</a></li>
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<li><a href="#exper">Experiments</a></li>
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<li><a href="#optandval">Optimization and Validation</a></li>
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<li><a href="#concl">Conclusion</a></li>
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</li>
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<li class="list-group-item">
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<a class="dropdown-toggle" href="#PHsenscir">Plant-Human: Sensor Circuit</a>
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<li><a href="#PHdeter">Deterministic</a></li>
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<li><a href="#PHstoch">Stochastic</a></li>
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</li>
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<li class="list-group-item">
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<a class="dropdown-toggle" href="#experdata">Experimental Data</a>
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<ul>
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<li><a href="#opto">Optogenetic Circuit</a></li>
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<li><a href="#sens">Sensor Circuit</a></li>
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<li class="list-group-item active"><a href="#valid">Validation</a></li>
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<li class="list-group-item active"><a href="#concls">Conclusions</a></li>
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<!--APARTADO-->
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<div id="section1" class="container">
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<div class="heading-color">
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<h2><span>INTRODUCTION</span></h2>
 +
</div>
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<p class="jopesangria">Modeling our gene circuits is of paramount importance since it provides us with deep insight and prediction capability of the biological processes taking place in ChatterPlant. This way, we aim to break the traditional wall imposed by trial-error approaches, which often result in unnecessary or inconclusive experiments.</p>
 +
<p class="jopesangria">Mathematical models in synthetic biology contribute not only to generate empirically contrastable hypothesis but also to manage laboratory time and hardware resources efficiently. Furthermore, because of the understanding and foresight provided by modeling, tuning and programing ChatterPlant according to the necessities of certain situations is possible more than ever.</p>
 +
<div id="deterystcomod" class="heading-color jopesubapartado">
 +
<h4><span>DETERMINISTIC AND STOCHASTIC MODELS</span></h4>
 +
</div>
 +
<p class="jopesangria">In ChatterPlant we analyze the dynamic behavior of our biological system considering the biochemical species involved in a certain set of reactions. According to the degree of approximation to capture the dynamic behavior, we can differentiate two approaches:</p>
 +
<ol class="jopenumeracion">
 +
<li>
 +
<p class="jopesangria" style="margin-bottom: 0px !important;"><strong class="jopenegrita">Deterministic</strong>. Deterministic models do not take into account the natural randomness of the reactions. For each chemical species, the amount of molecules transformed within reactions only depends on the initial amount of molecules, reaction rates and stoichiometry relations.</p>
 +
<p class="jopesangria">The type of deterministic model that we implement is a system of Ordinary Differential Equations (ODEs)</p>
 +
</li>
 +
<li><strong class="jopenegrita">Stochastic</strong>. Inherent noise due to random events plays a relevant role in the dynamics. As a deterministic model does not capture noise, we use stochastic linear differential equations</li>
 +
</ol>
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<div class="divider"><!-- divider /ESTO ES LA BARRITA QUE SALE TRAS UN APARTADO NO SE PUEDE QUITAR/ --></div>
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</div>
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<!--/APARTADO-->
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<!--APARTADO-->
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<div id="overview" class="container">
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<div class="heading-color">
 +
<h2><span>OVERVIEW</span></h2>
 +
</div>
 +
<div id="what" class="heading-color jopesubapartado">
 +
<h4><span>WHAT WE ARE MODELING?</span></h4>
 +
</div>
 +
<p class="jopesangria">The SynBio-based design integrated in ChatterPlant is composed by two gene circuits. The analysis of both their single performance and their interaction with several factors (e.g. the cell medium, environment and ChatterBox), is basic to reach one of our main goals: a new sustainable and efficient agriculture system.</p>
 +
<p class="jopesangria">Our model comprises of:</p>
 +
<ol class="jopenumeracion">
 +
<li><strong class="jopenegrita">Optogenetic circuit</strong>. How long has to remain the light pulse in order to get a certain protein amount? How could be optimized the energetic supply of LEDs light in order to maximize a cycle of protein production? These questions among others arose to our minds as we were designing the LED’s system.</li>
 +
<li><strong class="jopenegrita">Sensor circuit</strong>. Bearing in mind the time span during which the biological sensor is transiently ON, it is mandatory to design a sampling rate test according to the plant’s periodic security necessities.</li>
 +
</ol>
 +
<div id="software" class="heading-color jopesubapartado">
 +
<h4><span>MODELING SOFTWARE MODULES</span></h4>
 +
</div>
 +
<p class="jopesangria">We start building the genetic circuits from basic modules, coupling them to generate the mathematical model of the whole system. As UPV_iGEM is an interdisciplinary team, most of the models generated in ChatterPlant are included in the modeling software tool and are represented by modules in an artistic graphic interface, for the purpose of introducing researchers to a more realistic conception of the engineering in biology, meanly, SynBio.</p>
 +
<div class="divider"><!-- divider --></div>
 +
</div>
 +
<!--/APARTADO-->
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<!--APARTADO-->
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<div id="HPoptcir" class="container">
 +
<div class="heading-color">
 +
<h2><span>HUMAN-PLANT: OPTOGENETIC CIRCUIT</span></h2>
 +
</div>
 +
<p class="jopesangria">Two constitutive modules express the E-PIF6 and PhyB-VP64 fusion proteins that regulate the output expression.</p>
 +
<img class="img-responsive" style="width:100%;margin-bottom: 10px;" src="https://static.igem.org/mediawiki/2017/c/cc/Figura1ModelingValencia.jpeg"/>
 +
<p class="jopesangria"><i class="jopecursiva">Constitutive modules representation of the fusion proteins E-PIF6 and PhyB-VP64.</i></p>
 +
<p class="jopesangria">E-PIF6 binds to the promoter’s operator. When red light (660 nm wavelength) LEDs are switched on, PhyB changes its conformation (PhyB*) and binds to PIF6.  Consequently, the transcription of the desired protein starts because of the RNAp recruitment by VP64.</p>
 +
<img class="img-responsive" style="width:100%;margin-bottom: 10px;" src="https://static.igem.org/mediawiki/2017/c/c8/Figura2ModelingValencia.jpeg"/>
 +
<p class="jopesangria"><i class="jopecursiva">Expression regulated by the transcriptional factors.</i></p>
 +
<p class="jopesangria">Far red light (740 nm wavelength) reverts PhyB* to its natural conformation (PhyB). This change stops de transcriptional activity of the third optogenetic circuit’s module.</p>
 +
<img class="img-responsive" style="width:100%;margin-bottom: 10px;" src="https://static.igem.org/mediawiki/2017/6/68/Figura3ModelingValencia.jpeg"/>
 +
<p class="jopesangria"><i class="jopecursiva">Switch off.</i></p>
 +
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<!--/APARTADO-->
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<h2><span>NOMBRE DEL APARTADO 4</span></h2>
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<p class="jopesangria"><strong class="jopenegrita"></strong> aquí va el texto.</p>
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<img class="float-right img-fluid" src="https://static.igem.org/mediawiki/2017/6/63/HardwareSafetyValencia.jpeg" style="width:400px !important" alt=""/>
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<p class="jopesangria">Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.</p>
 +
<p class="jopesangria">Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.</p>
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<div class="divider"><!-- divider --></div>
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<!--/APARTADO-->
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<h2><span>NOMBRE DEL APARTADO 6</span></h2>
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<p class="jopesangria"><strong class="jopenegrita"></strong> aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<h2><span>NOMBRE DEL APARTADO 7</span></h2>
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<p class="jopesangria"><strong class="jopenegrita"></strong> aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<div class="divider"><!-- divider --></div>
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<h2><span>NOMBRE DEL APARTADO 8</span></h2>
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<p class="jopesangria"><strong class="jopenegrita"></strong> aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<div class="divider"><!-- divider --></div>
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<p class="jopesangria"><strong class="jopenegrita"></strong> aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<h2><span>NOMBRE DEL APARTADO 10</span></h2>
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<p class="jopesangria"><strong class="jopenegrita"></strong> aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<p class="jopesangria"><strong class="jopenegrita">Ejemplo de texto en negrita</strong> aquí va el texto.</p>
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<p class="jopesangria">Aquí va el texto.</p>
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<p class="jopesangria"><i class="jopecursiva">Esto es un ejemplo de texto en italic</i></p>
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<p class="jopesangria">Aquí va el texto.</p>
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<img class="img-responsive" style="width:100%;margin-bottom: 20px;" src="https://static.igem.org/mediawiki/2017/8/83/LabSafetyPaulaValencia.jpeg"/>
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<img class="float-left img-fluid" src="https://static.igem.org/mediawiki/2017/6/63/HardwareSafetyValencia.jpeg" style="width:400px !important" alt=""/>
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<p class="jopesangria">Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.</p>
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<p class="jopesangria">Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.</p>
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Revision as of 18:31, 30 October 2017

Home • Dry Lab •

MODELING

INTRODUCTION

Modeling our gene circuits is of paramount importance since it provides us with deep insight and prediction capability of the biological processes taking place in ChatterPlant. This way, we aim to break the traditional wall imposed by trial-error approaches, which often result in unnecessary or inconclusive experiments.

Mathematical models in synthetic biology contribute not only to generate empirically contrastable hypothesis but also to manage laboratory time and hardware resources efficiently. Furthermore, because of the understanding and foresight provided by modeling, tuning and programing ChatterPlant according to the necessities of certain situations is possible more than ever.

DETERMINISTIC AND STOCHASTIC MODELS

In ChatterPlant we analyze the dynamic behavior of our biological system considering the biochemical species involved in a certain set of reactions. According to the degree of approximation to capture the dynamic behavior, we can differentiate two approaches:

  1. Deterministic. Deterministic models do not take into account the natural randomness of the reactions. For each chemical species, the amount of molecules transformed within reactions only depends on the initial amount of molecules, reaction rates and stoichiometry relations.

    The type of deterministic model that we implement is a system of Ordinary Differential Equations (ODEs)

  2. Stochastic. Inherent noise due to random events plays a relevant role in the dynamics. As a deterministic model does not capture noise, we use stochastic linear differential equations

OVERVIEW

WHAT WE ARE MODELING?

The SynBio-based design integrated in ChatterPlant is composed by two gene circuits. The analysis of both their single performance and their interaction with several factors (e.g. the cell medium, environment and ChatterBox), is basic to reach one of our main goals: a new sustainable and efficient agriculture system.

Our model comprises of:

  1. Optogenetic circuit. How long has to remain the light pulse in order to get a certain protein amount? How could be optimized the energetic supply of LEDs light in order to maximize a cycle of protein production? These questions among others arose to our minds as we were designing the LED’s system.
  2. Sensor circuit. Bearing in mind the time span during which the biological sensor is transiently ON, it is mandatory to design a sampling rate test according to the plant’s periodic security necessities.

MODELING SOFTWARE MODULES

We start building the genetic circuits from basic modules, coupling them to generate the mathematical model of the whole system. As UPV_iGEM is an interdisciplinary team, most of the models generated in ChatterPlant are included in the modeling software tool and are represented by modules in an artistic graphic interface, for the purpose of introducing researchers to a more realistic conception of the engineering in biology, meanly, SynBio.

HUMAN-PLANT: OPTOGENETIC CIRCUIT

Two constitutive modules express the E-PIF6 and PhyB-VP64 fusion proteins that regulate the output expression.

Constitutive modules representation of the fusion proteins E-PIF6 and PhyB-VP64.

E-PIF6 binds to the promoter’s operator. When red light (660 nm wavelength) LEDs are switched on, PhyB changes its conformation (PhyB*) and binds to PIF6. Consequently, the transcription of the desired protein starts because of the RNAp recruitment by VP64.

Expression regulated by the transcriptional factors.

Far red light (740 nm wavelength) reverts PhyB* to its natural conformation (PhyB). This change stops de transcriptional activity of the third optogenetic circuit’s module.

Switch off.

NOMBRE DEL APARTADO 4

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Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

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NOMBRE DEL APARTADO 8

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NOMBRE DEL APARTADO 10

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Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.